Synthetic Biology Engineering Research Center

Synberc Blog

  • Kevin Costa |

    Karen Ochoa is a senior at Oakland Technical High School and an iCLEM 2014 Alumna. After spending the summer with us at JBEI, Karen shared this personal statement with us at the iCLEM final presentation on August 6, 2014. We share it here to give a sense of how programs like iCLEM can have an impact on a young person's life.

    As I walked into the building on my first day of work I dreaded every step I took, not because I was going to work, but because I had to meet new people.

    I was never good at making friends, and I was often isolated and forgotten. Well, if that was the case, then I would avoid making connections.

    As I entered the classroom I stayed quiet at first, trying to avoid connections but, eventually everyone started to talk to me. I was shocked, but I felt welcomed.

    The little things like taking me to the library, helping me with my personal statement, answering my questions, and a simple “good morning.” Those are some things that people take for granted, but for me it meant everything.

    Although the end is near, the chains of science turn into the chains of friendship. No. They are the chains of a family that bind us together.

    May it be the teachers, the undergraduates, post docs, or students, they are now my second family and JBEI has become my second home.

    No matter how far we travel or what path we take, the chains will always bind us.

    You might not be able to tell, but I am dreading this speech. Not because I am out of my comfort zone, but because as soon as I finish my speech, the closer we are to the end of the program. And I am afraid to say “good bye” and never have contact, so I will just say “see you soon.”

    Karen Ochoa
    Oakland Technical High School, Class of 2015
    iCLEM 2014 Alumna

  • Kevin Costa |

    Submitted to the Inter Academy Panel on May 23, 2014.

    Professor ter Meulen,

    We respond on behalf of the Synthetic Biology Engineering Research Center, an NSF-supported research consortium. Since 2006, Synberc has helped shape the field of synthetic biology, developed foundational technologies, educated emerging leaders, and promoted the responsible development of the field.

    Synberc supports the Inter Academy Panel’s recent statement on realizing the potential of synthetic biology. In particular:

    1. We endorse IAP recommendations on the relationship between foundational advances and practical applications. Much more foundational research is still needed to understand the biological and genomic underpinnings of synthetic biology that will allow us to address a broad range of challenges. We must continue to develop sound principles for assembling biological systems across different contexts, construct libraries of well-characterized components, and create the tools to design, build and test biological systems. Importantly, we must also develop the tools and technologies to provide policymakers and the public with the information needed to make science-based policy decisions about risk and uncertainty of real-world applications.

    2. We agree with the need to systematically prepare researchers to address the full spectrum of effects of synthetic biology. The next generation of biotechnologists will require not only extraordinary technical foundations, but also serious education on ethical, legal, societal and environmental issues, if the field is to develop justly. Synberc’s Policy & Practices program is working to that end by putting into practice systems to influence the selection and conduct of projects within Synberc. It also leads efforts with our public agencies and company partners to develop policies on governance and risk. Within Synberc-supported iGEM, the Policy & Practices program is helping to cultivate an ethos of responsibility and care among young synthetic biologists. The lessons learned within these efforts can and should be applied within other, broader contexts.

    3. We must expand the international dialogue to include diverse academic and public participants. Directing the research toward tangible social goods will require an active process involving academics across many disciplines, industry practitioners, funding agencies, as well as the workers, consumers, families, and patients who we hope to benefit. The field will develop justly only if practitioners listen carefully and respond to public concerns about improving regulations and sharing benefits. Scientists and non-scientists alike must be clear about the ethical issues created by synthetic biology, as well as the critical human needs that this biotechnology can help to address.

    4. We endorse the IAP call for a global policy and framework to support responsible science. Funding for the U.S.-based Synberc consortium is scheduled to come to a close at a time when it’s more important than ever to strengthen educational programs, support foundational research, and create inclusive venues on an international scale. We believe now is the time to expand this model into a larger and more inclusive organization to advance scientific and social progress. We would ask the major U.S. funding agencies (NSF, NIH, DOE, DARPA, and others) and their international counterparts to join with existing technologists, industrial partners, and civil society in committing to fund a long-term internationally coordinated program. The organization would serve as the primary conduit to coordinate international efforts and include an iterative roadmapping process to focus on global and topical issues important to and inclusive of both scientists and the public. The exact contours of this organization are to be determined, but models could include the Computing Community Consortium (www.ccc.org), the International Technology Roadmap for Semiconductors (www.itrs.net), and the International Society for Stem Cell Research (http://www.isscr.org/).

    We appreciate the IAP’s statement on realizing the global potential of synthetic biology. There is an undeniable need for a coordinated ecosystem of people and institutions if we are to responsibly advance this open and distributed technology for maximum public benefit. We look forward to working with members of the IAP and many, many others to sustain, promote and grow that ecosystem.

    Signed,

    Jay D. Keasling (Director), UC Berkeley
    J. Christopher Anderson, UC Berkeley
    Adam Arkin , UC Berkeley
    George Church, Harvard Medical School
    Tanja Kortemme, UC San Francisco
    Natalie Kuldell, MIT
    Wendell Lim, UC San Francisco
    Susan Marqusee, UC Berkeley
    Kenneth Oye, MIT
    Megan Palmer, Stanford University
    Kristala Jones Prather, MIT
    Pamela Silver, Harvard Medical School
    Christopher Voigt, MIT
    Ron Weiss, MIT

  • Kevin Costa |

    There seems to be a lot of commotion in the synthetic biology community these days about how to organize our research community at the national level. This is definitely true within Synberc, where our Sustainability Project has been critically assessing what is needed to responsibly advance the field.

    For all of the hullabaloo, there’s very little actual organizing going on at the national level. The field has defaulted into a “communities of practice” mode, where smaller groups of practitioners of a particular interest or expertise naturally come together to share information and experience, and have an opportunity to develop themselves personally and professionally, or to advance a particular agenda.

    Here are some specific examples of how the synthetic biology community has self-organized:

    • iGEM - The “world’s premiere synbio competition” but also an important testbed for educating synthetic biologists, creating a shared database of parts, and for learning how to screen projects for safety/security concerns. Probably the most successful effort to organize the synbio community not just in the US but worldwide.
    • SynBioBeta - A recent but highly successful effort led by one organizing dynamo (John Cumbers, Santa Clara University/NASA Ames) that is bringing together small start-up companies and other entrepreneurially minded interests to foster the “synthetic biology start-up ecosystem.”
    • BioBricks Foundation - An early pioneer in trying to bring together the synthetic biology community in more or less the mode of a professional society. BBF runs the SBX.0 International Conference Series, which is the synbio community’s primary conference. BBF has also led a call for technical comments that led to the development of a BioBricks Public Agreement (BPA) to enable easier sharing of biological parts.
    • The DIYbio 'movement' is a good example of how citizen scientists and enthusiasts are organizing themselves at the very local levels -- the DIYbio community has not yet developed a strong guild at the national level, but the potential appears to be there.
    • Synberc - The US’s first and largest single effort to bring together leading researchers and universities to establish the scientific and engineering foundations of synthetic biology. It too was generated at the grassroots level by a group of like-minded researchers, rather than by a national fiat.

    One more important way in which the community is organizing itself: A crop of synthetic biology centers has blossomed at individual universities:

    The formation of these centers suggest that the community is hungry for organizational entities that last over many years and help researchers from diverse backgrounds come together to pursue shared research aims.

    Zooming back out to the national level, the basis set of leaders in synthetic biology are often recombined in different ways to address different problems in different contexts. For example, many of the experts involved in a NAS study on technical roadmaps are likely to be seen at another study on the ethical, legal and social ramifications of synthetic biology. The basis set of leaders is slowing growing outward as the field identifies new opportunities/challenges and becomes aware of and comfortable with others from different research communities. As with any highly multidisciplinary endeavor, the challenge for our community is to enable and encourage diverse practitioners with shared goals to come together to solve problems we cannot solve independently.

    In the UK, the scientific community has had better success in organizing itself at the national level, especially through the UK Roadmap process. One might argue about the practical value of the technology and society roadmap that such efforts produce, but the roadmap itself is probably not as important as bringing together new assemblages of scientists, policymakers, funders, and other stakeholders to think about the opportunities and challenges of synthetic biology from many perspectives. The report accompanying the roadmap has a number of important insights (IMHO) and did seem to result in the national synergy in synbio that the UK is now experiencing.

    Given the current status of organizing in the US and the need to develop a more coordinated framework, one might consider something like a spoke-and-hub model for getting there. In a sense, this is what Synberc is. The universities are bound together loosely by Synberc. The colleges and their investigators are free to pursue independent projects and even engage in cooperative competition, yet they can leverage Synberc infrastructure for thinking about "problems of the commons". These include strategic roadmapping, responsible innovation, education and workforce development, industry liaison (e.g., creating a one-stop shop for industry members to interact with leaders of the field), addressing intellectual property concerns, metrology and standards, communications & advocacy (enabling the community to speak with a common voice), and simply building community through regular symposia and workshops. Given the proliferation of “communities of practice” across the U.S. in synthetic biology, an elastic organization may be the only kind that can accommodate such a wide range of researchers and organizations.

  • Linda Kahl |

    Linda KahlOn July 13, 2013 the U.S. Supreme Court issued their decision in Association for Molecular Pathology v. Myriad Genetics, Inc. Naturally, this decision has sparked much discussion amongst the synthetic biology research community. What does this decision mean with regard to the patentability of synthetic constructs created from natural DNA sequences? Does this decision mean that the information contained within DNA sequences is patentable? And, ultimately, how will this decision affect innovation in synthetic biology?

    It is important to keep in mind that the court limited their decision to only one inquiry under U.S. patent law: Does isolated DNA or cDNA constitute patentable subject matter under 35 USC 101? The short answer is: NO for isolated DNA based on natural sequences, and MAYBE for cDNA molecules - see end of first paragraph, page 17.

    The court specifically expressed no opinion whether cDNA satisfies the other requirements for patentability such as novelty (35 USC 102), non-obviousness (35 USC 103), and enablement/definiteness (35 USC 112) - see footnote 9.

    As is typical of U.S. Supreme Court decisions, the full impact will be become more apparent as the lower courts interpret this decision in subsequent cases. While we may not yet have answers to all of our questions, we do have more certainty today than we did before.

    What we know for sure is that this decision renders invalid any claim with the structure “isolated DNA having SEQ ID NO: 1”

  • Christina Agapakis |

    ChristinaSynthetic biology is often referred to as "the field of the future," the foundation of a "third industrial revolution" that will change the way we produce fuelsmaterialsmedicines, as well as the way we produce knowledge of biological systems. But while the self-consciously revolutionary language of synthetic biology declares a change of the industrial status quo, the metaphors we rely on are explicit references to the successful revolutions of past industrial technologies.

    The term synthetic biology echoes the successes of synthetic chemistry, while the guiding concept of standardization in genetic components is modeled on 19th century standardization of interchangeable parts. Industrial metaphors mix further as we climb the abstraction hierarchy; genetic parts are assembled to fit into a cellular chassis, creating logic gates and circuits that can compute biological information, leading to the control of cellular factories.

    der menschThese metaphors help us to understand how an industrial revolution might emerge from a biology lab, showing a possible path from ideas to industry. Like the "horseless carriage," perhaps the analogies of living cells to computers give us a sense of familiarity with a technology whose potential we have not yet fully grasped. Industrial metaphors have long played a role in how we understand biology and the human body, from Fritz Kahn’s 1927 paintings of “Man as Industrial Palace” to  analogies between brains and computers. By referencing the products and methods of previous industrial revolutions, synthetic biology aims not only to aid understanding but also to demonstrate the future potential of the field. These metaphors draw the projected lines of Moore's exponential increase as strands of DNA, imagining analogous and expanding industries based on carbon and sunlight rather than silicon and fossil fuels. 

    Kuhn SSRHow will this revolutionary transition happen? What conditions are necessary to foster such a change? As synthetic biology is largely still a laboratory rather than industrial enterprise, perhaps Thomas Kuhn's The Structure of Scientific Revolutions, can provide a useful framework for understanding the structure of the promised techno-scientific-industrial revolution of synthetic biology. Based on his analysis of the history of chemistry and physics, Kuhn argues that the evolution of scientific knowledge proceeds by punctuated equilibrium — periods of "normal science" interrupted by scientific revolutions, paradigm shifts that change the nature of the questions being asked and the "puzzles" being solved. Paradigms shift after the accumulated weight of unexpected results becomes too large, when facts that don’t fit the model begin to open new questions and when the "failure of existing rules is the prelude to a search for new ones."

    Some of the failures of modern industry are explicit starting points for synthetic biology projects, like engineered bacteria that can sense or consume industrial pollutants, but norevolution can address all the failures of the paradigms that came before. For scientific revolutions, Kuhn writes, "To be accepted as paradigm, a theory must seem better than its competitors, but it need not, and in fact never does, explain all the facts with which it can be confronted." What problems can synthetic biology solve and what problems are missed, outside of the paradigmatic umbrella of biotechnology? What new problems might arise with a biology-based industrial revolution?

    These are difficult and important questions with no clear answer, questions that we ask ourselves when we talk about risk, implications, and outcomes of new technologies. But perhaps there is a deeper question that emerges when we look at synthetic biology through a Kuhnian lens: by working to solve the problems of current industry, replacing or cleaning up after polluting chemical factories with microscopic cellular factories, are we simply replicating the old paradigm with a biological tint? Are we talking revolution while just solving puzzles?

    Industrial metaphors for biological systems are being inverted, but the industrial paradigm remains: “Man as Industrial Palace” becomes “Industrial Palace in a Cell.” How can a biologically driven industry change these metaphors, change the way we make things and the way we do things that takes biology on its own terms, that changes the paradigm through which we see the world?

    Within synthetic biology, programs that I’ve been involved with such as Synthetic Aesthetics and the Synthetic Biology Leadership Excellence Accelerator Program (LEAP)--sponsored by Synberc's Practices thrust--are efforts to integrate new questions, metaphors, and paradigms into the research goals and visions of synthetic biologists. Synthetic Aesthetics joins artists and designers with scientists and engineers to consider not just implications of the products of synthetic biology but to reconsider what those products might be—the metaphors that we use to understand and design nature. LEAP has different but complementary goals, bringing together scientists and engineers in academia and industry with experts from policy, ethics, economics, and law and providing a space to creatively consider what it would mean for synthetic biology to work in the public interest.

    Both programs encourage those involved with synthetic biology to think beyond existing paradigms, both in science and industry. Conversations like these may help us to push beyond the industrial metaphors that we depend on when we talk about the potential of synthetic biology, providing us with new paradigms that can be truly revolutionary.

    ###

    Tune into Christina's regular blog at Scientific American. 

  • Linda Kahl |

    It’s a particularly exciting time for synthetic biology and for developments in intellectual property law.  Advances in the engineering of biology are deepening our understanding of how biological systems work and leading to new applications that could help promote human health and preserve the environment.  At the same time, tremendous advances in patent law are changing the way in which innovators seek protection for their intellectual property rights.

    The sweeping reforms to U.S. patent law brought about by the Leahy-Smith America Invents Act have created new opportunities and challenges for the synthetic biology research community.  On March 16th of this year the U.S. transitioned to a “first-inventor-to-file” priority system for patents, which is more aligned with the patent laws of other countries and will impact the strategic choices made by synthetic biology researchers seeking patent protection for their inventions.  

    Other exciting changes to U.S. patent law include crowdsourcing the examination of patent applications as well as broadening public participation in the post-grant review of issued patents.  These changes open up new possibilities for the synthetic biology research community to engage with the U.S. patent system and help ensure that patent protection is awarded only for inventions that truly merit a 20-year grant of monopoly rights.

    Court decisions affecting the interpretation of patent laws also may impact innovation in synthetic biology.  One case currently before the U.S. Supreme Court – Association for Molecular Pathology v. Myriad Genetics, Inc. – addresses the patentability of isolated DNA and cDNA molecules. While the Myriad case specifically focuses on DNA derived from human genes, the decision could shed light on the patentability of synthetic DNA derived from natural sources.  Oral arguments for the Myriad case are scheduled to take place on April 15th.

    Another case currently before the U.S. Supreme Court – Bowman v. Monsanto, Inc. – examines whether patent holders can enforce their patent rights on the products of self-replicating technologies after an authorized sale. The Bowman case is specifically looking at seeds from genetically modified plants, but self-replicating technologies abound in synthetic biology and the decision could impact the commercial development of useful products and constructive applications of synthetic biology. Oral arguments for the Bowman case were held on February 19th and a decision is expected by June.

    Here at Synberc, we are focusing on how property rights can best be applied and adapted to promote innovation in synthetic biology. We’re conducting a survey of the enabling technologies of synthetic biology so that we and others can systematically investigate the property rights associated with these technologies. We’re also developing a portfolio of options that will explore possible legislative changes as well as policy initiatives and community actions to more effectively work within the existing patent-based legal framework. We anticipate these options will not present a complete solution for all the property rights issues encountered in the emerging field of synthetic biology, but instead will serve to inform and contribute to broader discussions about the optimal use of property rights to promote innovation in synthetic biology and biotechnology, more generally.

    Linda Kahl, Ph.D., J.D.
    Legal Scholar, Synberc

  • Jay Keasling |

    Hello and welcome to our blog! Here you'll find informative opinion pieces about a range of issues in the field of synthetic biolgy, researcher profiles, and helpful resources in the form of both videos and text. Please join us here each week for commentary created by and for members of our community.

    Stay tuned for Linda Kahl's blog next week, where she discusses U.S. patent law reform and current U.S. Supreme Court cases that may impact the ways in which DNA might be patented, as well as whether patent holders can enforce their patent rights on the products of self-replicating technologies after an authorized sale.

    Also on deck is a blog from Christina Agapakis on the impact of Synberc's Leadership Excellence Accelerator Program.

    If you'd like to contribute a posting, please contact Kevin Costa (kcosta@berkeley.edu) for submission guidelines. We're looking forward to hearing from all of the voices in our community!

    Jay Keasling
    Director, Synberc